The characterization and validation of regulated cell death-related genes in chronic rhinosinusitis with nasal polyps
Hong-Xia Li1, Jing Fei2, Wei Xu2
1Department of Otolaryngology-Head and Neck Surgery, the Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646000, China; Metabolic Vascular Diseases Key Laboratory of Sichuan Province, and Metabolic Vascular Diseases Key Laboratory of Sichuan-Chongqing Cooperation, Luzhou, Sichuan 646000, China.
Background:
Regulated cell death (RCD), a genetically controlled process mediated by specialized molecular pathways (commonly termed programmed cell death), plays pivotal roles in diverse pathophysiological processes. However, the landscape and functional implications of RCD subtypes in chronic rhinosinusitis with nasal polyps (CRSwNP) remain poorly characterized. This study aimed to systematically investigate the involvement of RCD mechanisms in the pathogenesis and progression of CRSwNP.
Methods:
Transcriptomic datasets (GSE136825, GSE23552, GSE198950, GSE196169, GSE156285) related to CRSwNP were retrieved from the Gene Expression Omnibus (GEO) database. A comprehensive panel of 18 RCD-associated gene sets was compiled through a systematic literature review. Gene set variation analysis (GSVA) was employed to profile RCD activation patterns in CRSwNP. Integrative bioinformatics approaches including weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) regression were implemented to identify hub RCD-related genes and construct a cell death index (CDI). Single-cell RNA sequencing (scRNA-seq) data were analyzed to map RCD dynamics across cellular subpopulations. Clinical validation was performed using qRT-PCR quantification of key genes in nasal polyp/inferior turbinate tissues, with the concurrent assessment of symptom severity via visual analogue scale (VAS) scores.
Results:
GSVA revealed significant upregulation of 8 RCD subtypes in CRSwNP: apoptosis, ferroptosis, necroptosis, entotic cell death, lysosome-dependent cell death, NETosis, immunogenic cell death, and anoikis. Pathway enrichment analysis demonstrated that RCD-related differentially expressed genes were predominantly involved in epithelial-mesenchymal transition (EMT) and immune-inflammatory regulation. Furthermore, the WGCNA algorithm and LASSO analysis identified 8 key cell death genes (PTHLH, GRINA, S100A9, SCG2, HMOX1, RNF183, TYROBP, SEMA7A), which were utilized to construct the cell death-related index (CDI). In training and validation cohorts, the CDI was significantly elevated in CRSwNP compared to control and exhibited high diagnostic performance, with elevated scores correlating with enhanced immune cell infiltration. Single-cell resolution analysis uncovered cell type-specific RCD activation patterns. Clinical validation confirmed significantly higher expression of S100A9, PTHLH, and HMOX1 in eosinophilic versus non-eosinophilic polyps. Notably, expression levels of PTHLH, S100A9, HMOX1, GRINA, and TYROBP showed strong positive correlations with VAS scores.
Conclusions:
Our investigation delineates an RCD activation signature in CRSwNP pathogenesis, characterized by 8 key cell death modalities and their regulatory genes. The novel CDI exhibits promising diagnostic potential, while mechanistic insights suggest RCD pathways may drive disease progression through EMT potentiation and inflammatory cascade amplification. These findings provide a framework for developing RCD-targeted therapeutic strategies in CRSwNP.
Insights
This study reveals 8 regulated cell death (RCD) subtypes are active in chronic rhinosinusitis with nasal polyps (CRSwNP), with a new index showing diagnostic potential for this complex airway disease.
Area of Science:
- Molecular Biology
- Immunology
- Pathophysiology
Background:
- Regulated cell death (RCD) pathways are crucial in various diseases, but their role in chronic rhinosinusitis with nasal polyps (CRSwNP) is not well understood.
- Investigating RCD mechanisms is essential for understanding CRSwNP pathogenesis and progression.
Purpose of the Study:
- To systematically investigate the involvement and functional implications of diverse RCD subtypes in CRSwNP.
- To identify key RCD-related genes and develop a diagnostic index for CRSwNP.
Main Methods:
- Utilized transcriptomic datasets from Gene Expression Omnibus (GEO) and compiled RCD gene sets.
- Employed Gene Set Variation Analysis (GSVA), Weighted Gene Co-expression Network Analysis (WGCNA), and LASSO regression to identify RCD patterns and hub genes.
- Conducted single-cell RNA sequencing (scRNA-seq) for cell-type specific analysis and clinical validation using qRT-PCR and VAS scores.
Main Results:
- Identified significant upregulation of 8 RCD subtypes in CRSwNP, including apoptosis, ferroptosis, and necroptosis.
- Discovered RCD-related genes are involved in epithelial-mesenchymal transition (EMT) and immune-inflammatory regulation.
- Developed a novel cell death index (CDI) using 8 key genes (PTHLH, GRINA, S100A9, SCG2, HMOX1, RNF183, TYROBP, SEMA7A) that demonstrated high diagnostic performance and correlated with disease severity and immune cell infiltration.
Conclusions:
- Established an RCD activation signature in CRSwNP, highlighting 8 key cell death modalities and their regulatory genes.
- The novel CDI shows promise as a diagnostic tool for CRSwNP.
- RCD pathways likely contribute to CRSwNP progression via EMT and amplified inflammation, offering potential therapeutic targets.
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